| 167-hh-4-8-25-50 |
| ID: | 1485077531 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 398 (165) | ||
| Sequences: | 7078 (5707.2) | ||
| Seq/Len: | 42.897 | ||
| Nf(neff/√len): | 444.3 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 42.897).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 301_F | 328_T | 3.301 | 1.00 |
| 225_E | 268_K | 3.051 | 1.00 |
| 290_L | 304_R | 2.649 | 1.00 |
| 302_L | 325_V | 2.588 | 1.00 |
| 208_G | 247_N | 2.554 | 1.00 |
| 268_K | 272_L | 2.552 | 1.00 |
| 217_P | 271_F | 2.542 | 1.00 |
| 224_L | 228_L | 2.491 | 1.00 |
| 296_E | 304_R | 2.370 | 1.00 |
| 292_Q | 330_Q | 2.163 | 1.00 |
| 217_P | 221_L | 2.030 | 1.00 |
| 345_L | 349_I | 2.011 | 1.00 |
| 228_L | 238_W | 1.965 | 1.00 |
| 336_F | 339_H | 1.947 | 1.00 |
| 269_K | 273_Q | 1.873 | 1.00 |
| 297_P | 300_Q | 1.812 | 1.00 |
| 221_L | 272_L | 1.792 | 1.00 |
| 221_L | 268_K | 1.783 | 1.00 |
| 322_I | 348_L | 1.781 | 1.00 |
| 235_E | 238_W | 1.766 | 1.00 |
| 228_L | 233_G | 1.753 | 1.00 |
| 344_T | 347_Q | 1.734 | 1.00 |
| 242_I | 267_F | 1.729 | 1.00 |
| 235_E | 265_V | 1.706 | 1.00 |
| 301_F | 305_K | 1.701 | 1.00 |
| 239_L | 267_F | 1.696 | 1.00 |
| 290_L | 296_E | 1.630 | 1.00 |
| 305_K | 325_V | 1.624 | 1.00 |
| 304_R | 307_D | 1.602 | 1.00 |
| 217_P | 272_L | 1.598 | 1.00 |
| 347_Q | 350_Q | 1.519 | 1.00 |
| 325_V | 352_G | 1.516 | 1.00 |
| 289_D | 324_Y | 1.478 | 1.00 |
| 302_L | 349_I | 1.469 | 1.00 |
| 284_I | 287_E | 1.467 | 1.00 |
| 264_W | 268_K | 1.456 | 1.00 |
| 224_L | 242_I | 1.450 | 1.00 |
| 210_D | 247_N | 1.446 | 1.00 |
| 289_D | 323_Q | 1.437 | 1.00 |
| 243_Q | 254_W | 1.380 | 0.99 |
| 284_I | 311_T | 1.366 | 0.99 |
| 286_R | 327_G | 1.316 | 0.99 |
| 270_A | 273_Q | 1.313 | 0.99 |
| 265_V | 269_K | 1.312 | 0.99 |
| 290_L | 293_K | 1.302 | 0.99 |
| 326_V | 334_K | 1.300 | 0.99 |
| 289_D | 327_G | 1.275 | 0.99 |
| 288_L | 324_Y | 1.268 | 0.99 |
| 298_L | 352_G | 1.261 | 0.99 |
| 318_E | 321_V | 1.250 | 0.99 |
| 227_Y | 241_Q | 1.248 | 0.99 |
| 325_V | 328_T | 1.246 | 0.98 |
| 325_V | 348_L | 1.245 | 0.98 |
| 287_E | 308_L | 1.245 | 0.98 |
| 238_W | 264_W | 1.242 | 0.98 |
| 263_S | 266_E | 1.218 | 0.98 |
| 355_V | 359_L | 1.212 | 0.98 |
| 242_I | 264_W | 1.197 | 0.98 |
| 299_D | 353_L | 1.190 | 0.98 |
| 346_E | 350_Q | 1.187 | 0.98 |
| 222_S | 255_E | 1.187 | 0.98 |
| 217_P | 220_F | 1.182 | 0.98 |
| 309_Y | 321_V | 1.165 | 0.97 |
| 220_F | 245_H | 1.159 | 0.97 |
| 305_K | 309_Y | 1.156 | 0.97 |
| 285_Q | 323_Q | 1.153 | 0.97 |
| 229_R | 240_S | 1.126 | 0.97 |
| 317_E | 320_E | 1.124 | 0.97 |
| 356_Q | 360_E | 1.103 | 0.96 |
| 251_K | 255_E | 1.101 | 0.96 |
| 272_L | 276_E | 1.096 | 0.96 |
| 206_S | 245_H | 1.055 | 0.95 |
| 254_W | 267_F | 1.055 | 0.95 |
| 325_V | 329_L | 1.039 | 0.94 |
| 351_R | 354_E | 1.039 | 0.94 |
| 222_S | 251_K | 1.039 | 0.94 |
| 242_I | 271_F | 1.020 | 0.93 |
| 226_E | 251_K | 1.000 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4x3iA | 1 | 0 | 98.4 | 0.913 | Contact Map |
| 4x3xA | 1 | 0 | 98 | 0.921 | Contact Map |
| 4bhxA | 2 | 0.2111 | 86.6 | 0.957 | Contact Map |
| 3g21A | 1 | 0.1834 | 75.6 | 0.962 | Contact Map |
| 3g1gA | 2 | 0.1834 | 70.9 | 0.963 | Contact Map |
| 4e6sA | 1 | 0.1935 | 66.4 | 0.964 | Contact Map |
| 3ds4A | 2 | 0.1859 | 65.3 | 0.965 | Contact Map |
| 2fi2A | 2 | 0.2186 | 61.1 | 0.966 | Contact Map |
| 4ph1A | 3 | 0 | 57 | 0.966 | Contact Map |
| 3lhrA | 2 | 0.2161 | 56.4 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)